Cakan Lab. on Zebrafish Models

Overview

Zebrafish is a widely used, robust vertebrate model that is accessible for genetic modification, well suited for imaging, easy to manipulate, has a short generation time and low cost. Zebrafish has been increasingly used for disease modeling and cancer studies, and it has come forward as an attractive model for drug discovery and personalized medicine studies in recent years. Our group aims to develop novel zebrafish models and technology that will contribute to the zebrafish reseach mainly in the field of disease research and personalized medicine. 

Disease Models

CANCER MODELS:

Zebrafish tumors are strikingly similar to human tumors both genetically and pathologically. We generate zebrafish “humanized tumors” by overexpression of human oncogenes in selected tissues such as melanocytes and liver. Various genetic tools allow us to create time and space controlled expression of such oncogenes, in significantly shorter time and reduced cost than rodent models. Xenotrasnplantation of human cancer cells to zebrafish host is another technology we use to facilitate cancer studies. We apply and improve this technology to study cancer metastasis, angiogenesis and drug response. In long term we aim to develop robust patient derived xenografts (PDX) methodology and use it as a tool for personalized medicine in collaboration with local oncologists.

RARE DISEASE MODELS:

Zebrafish offers several advantages for rare disease modeling, and drug discovery. We are using CRISPR/Cas9 technology to generate mutations in disease genes. We collaborate with clinicians to generate genetic models of rare diseases in zebrafish. We are particularly interested in diseases that are more common in Turkey due to consanguinity.

The Group

Group Members

Cakan Lab. on Zebrafish Models

Research Group Leader

Gülçin ÇAKAN AKDOĞAN
gulcin.cakan@ibg.edu.tr
+90 232 299 41 00 (5261)
+9 02322994142

Emine GELİNCİ R&D Personnel  emine.gelinci@ibg.edu.tr
+90 232 299 41 00 (5262)

Merve BAŞOL PhD Student  merve.basol@ibg.edu.tr


Büşra KORKMAZ Researcher  busra.korkmaz@ibg.edu.tr


Mehmet Cem ÖZKAN Undergraduate Student  cem.ozkan@ibg.edu.tr


Helin ÖZAKTAŞ MSc Student  helin.ozaktas@ibg.edu.tr


Özlem EREZ Researcher  ozlem.erez@ibg.edu.tr


Gülten KURU Post-Doc Researcher  gulten.kuru@ibg.edu.tr


Saadet Nur YERSEL Undergraduate Student  None


Bahar SİNCAR Undergraduate Student  None


Former Members

Meryem ÖZAYDIN Care Taker  meryem.ozaydin@ibg.edu.tr


Mehmet Can KILIÇ Undergraduate Student  mehmetcan.kilic@msfr.ibg.edu.tr


Esra ERSÖZ GÜLSEVEN MSc Student  esra.ersoz@ibg.edu.tr


Merve BAŞOL MSc Student  merve.basol@ibg.edu.tr


Büşra KORKMAZ Visiting Student  busra.korkmaz@ibg.edu.tr


Ebru ÖNAL MSc Student  ebru.onal@ibg.edu.tr


Ekin DEMİRBAŞ MSc Student  ekin.demirbas@msfr.ibg.edu.tr


Khalid ABDALLA Researcher  khalid.abdalla@ibg.edu.tr


Ebru ÖNAL MSc Student  ebru.onal@ibg.edu.tr


Çiğdem KARAKOYUN Post-Doc Researcher  cigdem.karakoyun@ibg.edu.tr


Meryem ÖZAYDIN Care Taker  meryem.ozaydin@ibg.edu.tr


Ege Seray CEYHAN Undergraduate Student  seray.ceyhan@msfr.ibg.edu.tr


Muhammet MEMON PhD Student  muhammet.memon@msfr.ibg.edu.tr


Neşe BAYSAN MSc Student  nese.baysan@msfr.ibg.edu.tr


Metehan GÜZELKAYA Undergraduate Student  metehan.guzelkaya@ibg.edu.tr


Neşe BAYSAN MSc Student  nese.baysan@msfr.ibg.edu.tr


Sude GÜNEŞ Undergraduate Student  sude.gunes@msfr.ibg.edu.tr


Rabia ALTINTAŞ Undergraduate Student  rabia.altintas@ibg.edu.tr


Ebru ÖNAL Researcher  ebru.onal@ibg.edu.tr


Sümeyra Çiğdem SÖZER PhD Student  sumeyra.sozer@ibg.edu.tr


Helin ÖZAKTAŞ Undergraduate Student  helin.ozaktas@ibg.edu.tr


Olga ESTEVES VAZQUEZ PhD Student  None


Özlem EREZ Visiting Researcher  ozlem.erez@ibg.edu.tr


Ebru ÖNAL MSc Student  ebru.onal@ibg.edu.tr


Serhat SONGÖREN MSc Student  serhat.songoren@ibg.edu.tr


Özlem EREZ Technician  ozlem.erez@ibg.edu.tr


Esra ERSÖZ GÜLSEVEN Researcher  esra.ersoz@ibg.edu.tr


Ecem SAYGILI Visiting Researcher  ecem.saygili@ibg.edu.tr


Özlem EREZ Technician  ozlem.erez@ibg.edu.tr


Güneş TOK MSc Student  gunes.tok@ibg.edu.tr


Sezin ÇAKAL MSc Student  sezin.cakal@ibg.edu.tr


Rana ACAR Visiting Student  rana.acar@ibg.edu.tr


Zeynep AKÇOR Undergraduate Student  zeynep.akcor@ibg.edu.tr


Selected Publications

Lucena MI, Villanueva-Paz M, Alvarez-Alvarez I, Aithal GP, Björnsson ES, Cakan-Akdogan G, Cubero FJ, Esteves F, Falcon-Perez JM, Fromenty B, Garcia-Ruiz C, Grove JI, Konu O, Kranendonk M, Kullak-Ublick GA, Miranda JP, Remesal-Doblado A, Sancho-Bru P, Nelson L, Andrade RJ, Daly AK, Fernandez-Checa JC. Roadmap to DILI research in Europe. A proposal from COST action ProEuroDILINet.. Pharmacological research. 2024 February ; 200 : 107046. doi:10.1016/j.phrs.2023.107046. Download

Argitekin E, Ersoz-Gulseven E, Cakan-Akdogan G, Akdogan Y. Dopamine-Conjugated Bovine Serum Albumin Nanoparticles Containing pH-Responsive Catechol-V(III) Coordination for In Vitro and In Vivo Drug Delivery.. Biomacromolecules. 2023 August ; 24 (8) : 3603-3618. doi:10.1021/acs.biomac.3c00363. Download

Guzelkaya M, Onal E, Gelinci E, Kumral A, Cakan-Akdogan G. A zebrafish model for studying the mechanisms of newborn hyperbilirubinemia and bilirubin-induced neurological damage.. Frontiers in cell and developmental biology. 2023 November ; 11 : 1275414. doi:10.3389/fcell.2023.1275414. Download

Arslan M, Karadag M, Onal E, Gelinci E, Cakan-Akdogan G, Kalyoncu S. Effect of non-repetitive linker on in vitro and in vivo properties of an anti-VEGF scFv.. Scientific reports. 2022 March ; 12 (1) : 5449. doi:10.1038/s41598-022-09324-4. Download

Yasar Akdogan, Sumeyra Cigdem Sozer , Cansu Akyol , Merve Basol , Cigdem Karakoyun, Gulcin Cakan-Akdogan*. Synthesis of albumin nanoparticles in a water-miscible ionic liquid system, and their applications for chlorambucil delivery to cancer cells. Journal of Molecular Liquids. 2022 December ; 367 (Part B) : 120575. doi:10.1016/j.molliq.2022.120575. Download

Gulcin Cakan-Akdogan*, Esra Ersoz, Emine Gelinci. An in vivo zebrafish model reveals circulating tumor cell targeting capacity of serum albumin nanoparticles. Journal of Drug Delivery Science and Technology. 2022 September ; 75 : 103658. doi:10.1016/j.jddst.2022.103658. Download

Evin Iscan, Umut Ekin, Gokhan Yildiz, Ozden Oz, Umur Keles, Aslı Suner, Gulcin Cakan-Akdogan, Gunes Ozhan, Marta Nekulova, Borivoj Vojtesek, Hamdiye Uzuner, Gökhan Karakülah, Hani Alotaibi and Mehmet Ozturk. TAp73β Can Promote Hepatocellular Carcinoma Dedifferentiation. Cancers. 2021 February ; 13 (4) : 783. doi:10.3390/cancers13040783. Download

Saniye Gul Kaya, Seniz Inanc-Surer, Gulcin Cakan-Akdogan, Gulgun Oktay, Canan Asli Utine, Sibel Kalyoncu. Roles of matrix metalloproteinases in the cornea: A special focus on macular corneal dystrophy. Medicine in Drug Discovery. 2021 September ; 11 : 100095. doi:10.1016/j.medidd.2021.100095. Download

Gurer DC, Erdogan İ, Ahmadov U, Basol M, Sweef O, Cakan-Akdogan G, Akgül B. Transcriptomics Profiling Identifies Cisplatin-Inducible Death Receptor 5 Antisense Long Non-coding RNA as a Modulator of Proliferation and Metastasis in HeLa Cells.. Frontiers in cell and developmental biology. 2021 August ; 9 : 2248. doi:10.3389/fcell.2021.688855. Download

Sumeyra Cigdem Sozer, Tugce OZmen Egesoy, Merve Basol, Gulcin Cakan-Akdogan, Yasar Akdogan. A simple desolvation method for production of cationic albumin nanoparticles with improved drug loading and cell uptake. Journal of Drug Delivery Science and Technology. 2020 December ; 60 : 101931. doi:10.1016/j.jddst.2020.101931. Download

Topel H, Bagirsakci E, Comez D, Bagci G, Cakan-Akdogan G, Atabey N. lncRNA HOTAIR overexpression induced downregulation of c-Met signaling promotes hybrid epithelial/mesenchymal phenotype in hepatocellular carcinoma cells.. Cell communication and signaling : CCS. 2020 July ; 18 (1) : 110. doi:10.1186/s12964-020-00602-0. Download

Begüm Demirkurt, Gulcin Cakan-Akdogan, Yasar Akdogan. Preparation of albumin nanoparticles in water-in-ionic liquid microemulsions. Journal of Molecular Liquids. 2019 December ; 295 : 117713. doi:10.1016/j.molliq.2019.111713. Download

Aysim Gunes, Ezgi Bagirsakci, Evin Iscan, Gulcin Cakan-Akdogan, Umut Aykutlu, Serif Senturk, Gunes Ozhan, Esra Erdal, Deniz Nart, Funda Yilmaz Barbet, Nese Atabey. Thioredoxin interacting protein promotes invasion in hepatocellular carcinoma. Oncotarget. 2018 ; 9 (96) : 36849-36866. doi:10.18632/oncotarget.26402. Download

Moraru A, Cakan-Akdogan G, Strassburger K, Males M, Mueller S, Jabs M, Muelleder M, Frejno M, Braeckman BP, Ralser M, Teleman AA. THADA Regulates the Organismal Balance between Energy Storage and Heat Production. Developmental cell. 2017 April ; 41 (1) : 72-81.e6. doi:10.1016/j.devcel.2017.03.016. Download

Akdogan Y, Emrullahoglu M, Tatlidil D, Ucuncu M, Cakan-Akdogan G. EPR studies of intermolecular interactions and competitive binding of drugs in a drug-BSA binding model. Physical chemistry chemical physics : PCCP. 2016 August ; 18 (32) : 22531-9. doi:10.1039/c6cp04137j. Download

Karakus, Erman; Cakan-Akdogan, Gulcin; Emrullahoglu, Mustafa. A guanidinium modified rhodamine-based fluorescent probe for in vitro/vivo imaging of gold ions. ANALYTICAL METHODS. 2015 ; 7 (19) : 8004-8008. doi:10.1039/c5ay01581b. Download

Pallares-Cartes C, Cakan-Akdogan G, Teleman AA. Tissue-specific coupling between insulin/IGF and TORC1 signaling via PRAS40 in Drosophila. Developmental cell. 2012 January ; 22 (1) : 172-82. doi:10.1016/j.devcel.2011.10.029. Download

Lecaudey V, Cakan-Akdogan G, Norton WH, Gilmour D. Dynamic Fgf signaling couples morphogenesis and migration in the zebrafish lateral line primordium. Development (Cambridge, England). 2008 August ; 135 (16) : 2695-705. doi:10.1242/dev.025981. Download

Total : 18

Selected Book Chapters

Zebra Balığı Kanser Modelleri ve Kişiselleştirilmiş Tıp Uygulamaları (2023). Zebra Balığının Model Organizma Olarak Kullanımı. Türkiye Klinikleri.

Total : 1

Selected Proceedings

Merve Arslan, Gulcin Cakan-Akdogan, Sibel Kalyoncu 2019, 'Antibody Engineerıng Approaches on Vernier Zone Residues to Develop Biobetter Antibody Therapeutics for Cancer Treatment', 2nd International Cancer & Ion Channels Congress, İzmir, Sept. 22, 2019 .

Total : 1

Projects

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Development of next-generation recombinant antibody fragments against VEGF for cancer therapy., Ongoing

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Target Specific Pan-Cancer Therapies (PAN-TER), Ongoing

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Investigation of the role of HGF/c-Met Pathway in tumor microenvironment during the progression of liver metastasis, Ongoing

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Su / iyonik sıvı mikroemülsiyonları içerisinde ilaç yüklü albümin nanoparçacıkların sentezi, karakte, Ongoing

The Scientific and Technological Research Council of Turkey - TUBITAK - RD : Zebra balığı mikroçevresinde meme ve melanoma kanseri hücrelerinin metastatik biyodağılımının haritalanması, Pre Submitted

Health Institutes of Turkey- TUSEB - RD : Zebrafish Patient Derived Xenograft Test for Personalized Medicine Applications in Ovarian Cancer Treatment, Funded, Not Started

European Union - RD : Halt-RONIN: Discovering chronic inflammation biomarkers that define key stages in the Healthy-to-NASH (non-alcoholic steatohepatitis) transition to inform early prevention and treatment strategies, Ongoing

Open Positions

We have open positions for researcher and research technician to work on newly fundend Horizon 2020 project. Candidates interested in liver diseases and zebrafish technology development shall send an email with CV, motivation letter and transcripts until 15.01.2023

 

Contact

Cakan Lab. on Zebrafish Models

Research Group Leader

Gülçin ÇAKAN AKDOĞAN
gulcin.cakan@ibg.edu.tr
+90 232 299 41 00 (5261)
+9 02322994142